Main tool : NCBI AMRFinderPlus
Additional tools:
- hmmer v3.3.2
- ncbi-blast+ v2.12.0
The database included at time of docker image build is 2022-12-19.1. More information can be found in the changes.txt on NCBI's FTP.
Full documentation: https://github.com/ncbi/amr/wiki
# list out the available organisms for the -O/--organism flag
$ Running: amrfinder -l
Software directory: '/amrfinder/'
Software version: 3.11.2
Database directory: '/amrfinder/data/2022-12-19.1'
Database version: 2022-12-19.1
Available --organism options: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter, Clostridioides_difficile, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae, Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae
# download Klebsiella oxytoca genome FASTA/FNA to use as a test
$ wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz"
# uncompress the FNA file
$ gzip -d GCA_003812925.1_ASM381292v1_genomic.fna.gz
# run amrfinder (nucleotide mode) on the uncompressed FNA file
$ amrfinder --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv
# part of output TSV
Name Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
GCA_003812925.1 NA CP033844.1 369234 370406 + oqxA multidrug efflux RND transporter periplasmic adaptor subunit OqxA core AMRAMR PHENICOL/QUINOLONE PHENICOL/QUINOLONE BLASTX 391 391 100.00 90.79 391 WP_002914189.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA NA NA
GCA_003812925.1 NA CP033844.1 370433 373582 + oqxB multidrug efflux RND transporter permease subunit OqxB core AMR AMR PHENICOL/QUINOLONE PHENICOL/QUINOLONE BLASTX 1050 1050 100.00 96.86 1050 WP_023323140.1 multidrug efflux RND transporter permease subunit OqxB15 NA NA
GCA_003812925.1 NA CP033844.1 636118 637917 - ybtQ yersiniabactin ABC transporter ATP-binding/permease protein YbtQ plus VIRULENCE VIRULENCE NA NA BLASTX 600 600 100.00 89.17 600 AAC69584.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA
GCA_003812925.1 NA CP033844.1 637913 639706 - ybtP yersiniabactin ABC transporter ATP-binding/permease protein YbtP plus VIRULENCE VIRULENCE NA NA BLASTX 598 600 99.67 89.30 598 CAA21388.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA
GCA_003812925.1 NA CP033844.1 3473617 3474798 + emrD multidrug efflux MFS transporter EmrD plus AMR AMR EFFLUX EFFLUX BLASTX 394 394 100.00 94.16 394 ACN65732.1 multidrug efflux MFS transporter EmrD NA NA
GCA_003812925.1 NA CP033844.1 5085488 5086357 - blaOXY-2-1 extended-spectrum class A beta-lactamase OXY-2-1 core AMR AMRBETA-LACTAM CEPHALOSPORIN ALLELEX 290 290 100.00 100.00 290 WP_032727905.1 extended-spectrum class A beta-lactamase OXY-2-1 NA NA
GCA_003812925.1 NA CP033845.1 5102 5632 - ant(2'')-Ia aminoglycoside nucleotidyltransferase ANT(2'')-Ia core AMR AMRAMINOGLYCOSIDE GENTAMICIN/KANAMYCIN/TOBRAMYCIN BLASTX 177 177 100.00 98.31 177 WP_000381803.1 aminoglycoside nucleotidyltransferase ANT(2'')-Ia NA NA
GCA_003812925.1 NA CP033846.1 748 1932 - tet(39) tetracycline efflux MFS transporter Tet(39) core AMR AMR TETRACYCLINETETRACYCLINE EXACTX 395 395 100.00 100.00 395 WP_004856455.1 tetracycline efflux MFS transporter Tet(39) NA NA